infercnv (version 1.3.3)

apply_median_filtering: apply_median_filtering

Description

Apply a median filtering to the expression matrix within each tumor bounds

Usage

apply_median_filtering(infercnv_obj, window_size = 7,
  on_observations = TRUE, on_references = TRUE)

Arguments

infercnv_obj

infercnv_object

window_size

Size of the window side centered on the data point to filter (default = 7).

on_observations

boolean (default=TRUE), run on observations data (tumor cells).

on_references

boolean (default=TRUE), run on references (normal cells).

Value

infercnv_obj with median filtering applied to observations

Examples

# NOT RUN {
# data(data)
# data(annots)
# data(genes)

# infercnv_obj <- infercnv::CreateInfercnvObject(raw_counts_matrix=data, 
#                                                gene_order_file=genes,
#                                                annotations_file=annots,
#                                                ref_group_names=c("normal"))

# infercnv_obj <- infercnv::run(infercnv_obj,
#                               cutoff=1,
#                               out_dir=tempfile(), 
#                               cluster_by_groups=TRUE, 
#                               denoise=TRUE,
#                               HMM=FALSE,
#                               num_threads=2,
#                               no_plot=TRUE)

data(infercnv_object)

infercnv_obj <- infercnv::apply_median_filtering(infercnv_obj)
# plot result object

# }